library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)
load(file = "lung_mich_curated.Rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1
## 0.0000000001
## MEISSNER_BRAIN_HCP_WITH_H3K27ME3
## 0.0002000001
## KIM_TIAL1_TARGETS
## 0.0002000001
## MUELLER_METHYLATED_IN_GLIOBLASTOMA
## 0.0004000001
## MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED
## 0.0008000001
## GU_PDEF_TARGETS_DN
## 0.0009000001
## CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP
## 0.0015000001
## WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN
## 0.0017000001
## HUPER_BREAST_BASAL_VS_LUMINAL_DN
## 0.0025000001
## CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN
## 0.0026000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 118
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 3
nominal_dcor_q_values_under_25
## SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1
## 0.0000002955
## MEISSNER_BRAIN_HCP_WITH_H3K27ME3
## 0.1970000985
## KIM_TIAL1_TARGETS
## 0.1970000985
nrow(gsea_results_significant)
## [1] 296
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 33
Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))
Mutually_identified_in_GSEA_dcor
## [1] "GU_PDEF_TARGETS_DN"
## [2] "HUPER_BREAST_BASAL_VS_LUMINAL_DN"
## [3] "SABATES_COLORECTAL_ADENOMA_UP"
## [4] "ENK_UV_RESPONSE_EPIDERMIS_UP"
## [5] "GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN"
## [6] "WOOD_EBV_EBNA1_TARGETS_DN"
## [7] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN"
## [8] "WU_CELL_MIGRATION"
## [9] "JAEGER_METASTASIS_DN"
## [10] "AMIT_SERUM_RESPONSE_480_MCF10A"
## [11] "HAHTOLA_CTCL_CUTANEOUS"
## [12] "BAE_BRCA1_TARGETS_UP"
## [13] "VANTVEER_BREAST_CANCER_ESR1_DN"
## [14] "ONDER_CDH1_TARGETS_2_DN"
## [15] "LI_LUNG_CANCER"
## [16] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"
## [17] "COLDREN_GEFITINIB_RESISTANCE_DN"
## [18] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"
## [19] "LEE_LIVER_CANCER_ACOX1_UP"
## [20] "JIANG_AGING_HYPOTHALAMUS_DN"
## [21] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP"
## [22] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"
## [23] "KIM_HYPOXIA"
## [24] "SESTO_RESPONSE_TO_UV_C1"
## [25] "BIOCARTA_CERAMIDE_PATHWAY"
## [26] "HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP"
## [27] "MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP"
## [28] "KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
## [29] "HAN_SATB1_TARGETS_UP"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 0
Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 | MEISSNER_BRAIN_HCP_WITH_H3K27ME3 | KIM_TIAL1_TARGETS | MUELLER_METHYLATED_IN_GLIOBLASTOMA | MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED | CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP | WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN | CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN | REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION | SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER | GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP | KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP | NABA_SECRETED_FACTORS | DORSAM_HOXA9_TARGETS_DN | DURAND_STROMA_NS_UP | ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP | DORN_ADENOVIRUS_INFECTION_12HR_UP | WANG_BARRETTS_ESOPHAGUS_UP | MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP | APPIERTO_RESPONSE_TO_FENRETINIDE_DN | PARK_APL_PATHOGENESIS_DN | SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN | SIMBULAN_UV_RESPONSE_NORMAL_DN | HUPER_BREAST_BASAL_VS_LUMINAL_UP | KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP | BENPORATH_PROLIFERATION | STEIN_ESRRA_TARGETS | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN | OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP | SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN | HENDRICKS_SMARCA4_TARGETS_UP | SANA_TNF_SIGNALING_DN | LEE_TARGETS_OF_PTCH1_AND_SUFU_DN | NABA_MATRISOME_ASSOCIATED | KEGG_PROPANOATE_METABOLISM | KAMIKUBO_MYELOID_CEBPA_NETWORK | VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN | VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP | MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED | BOYLAN_MULTIPLE_MYELOMA_D_DN | REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE | KEGG_CYSTEINE_AND_METHIONINE_METABOLISM | KEGG_PYRUVATE_METABOLISM | NAKAJIMA_EOSINOPHIL | ZHAN_MULTIPLE_MYELOMA_DN | HAHTOLA_SEZARY_SYNDROM_UP | KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP | ROSS_AML_WITH_PML_RARA_FUSION | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | TSUNODA_CISPLATIN_RESISTANCE_DN | HELLER_SILENCED_BY_METHYLATION_UP | VANTVEER_BREAST_CANCER_METASTASIS_UP | HAN_JNK_SINGALING_UP | REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING | DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN | JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP | WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP | STEARMAN_TUMOR_FIELD_EFFECT_UP | STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN | SU_PLACENTA | ANDERSEN_LIVER_CANCER_KRT19_UP | CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP | LINDVALL_IMMORTALIZED_BY_TERT_UP | BROWNE_HCMV_INFECTION_2HR_UP | BOYLAN_MULTIPLE_MYELOMA_PCA1_UP | MCDOWELL_ACUTE_LUNG_INJURY_UP | DELPUECH_FOXO3_TARGETS_UP | DOANE_RESPONSE_TO_ANDROGEN_UP | ABE_VEGFA_TARGETS_2HR | SANSOM_APC_TARGETS_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN | JIANG_AGING_CEREBRAL_CORTEX_DN | YAMAZAKI_TCEB3_TARGETS_DN | PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP | ABE_VEGFA_TARGETS_30MIN | ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP | DORN_ADENOVIRUS_INFECTION_48HR_DN | MOREIRA_RESPONSE_TO_TSA_UP | MALONEY_RESPONSE_TO_17AAG_DN | KAAB_FAILED_HEART_VENTRICLE_DN | ZAMORA_NOS2_TARGETS_UP | GALLUZZI_PERMEABILIZE_MITOCHONDRIA | HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN | SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5 | STEIN_ESR1_TARGETS | PAL_PRMT5_TARGETS_DN | SWEET_LUNG_CANCER_KRAS_UP | YANAGIHARA_ESX1_TARGETS | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.000 | 0.0002 | 0.0002 | 0.0004 | 0.0008 | 0.0015 | 0.0017 | 0.0026 | 0.0039 | 0.0044 | 0.0054 | 0.0054 | 0.0066 | 0.0069 | 0.0074 | 0.0075 | 0.0075 | 0.0079 | 0.0089 | 0.0102 | 0.0112 | 0.0112 | 0.0121 | 0.0129 | 0.0154 | 0.0167 | 0.0169 | 0.0169 | 0.0170 | 0.0182 | 0.0189 | 0.0198 | 0.0199 | 0.0200 | 0.0203 | 0.0204 | 0.0205 | 0.0214 | 0.0244 | 0.0246 | 0.0247 | 0.0259 | 0.0262 | 0.0263 | 0.0271 | 0.0280 | 0.0283 | 0.0292 | 0.0305 | 0.0305 | 0.0311 | 0.0317 | 0.0319 | 0.032 | 0.0321 | 0.0323 | 0.0326 | 0.0337 | 0.0342 | 0.0342 | 0.0344 | 0.0352 | 0.0358 | 0.0359 | 0.0362 | 0.0369 | 0.0392 | 0.0392 | 0.0400 | 0.0402 | 0.0404 | 0.0408 | 0.0412 | 0.0413 | 0.0416 | 0.0421 | 0.0424 | 0.0431 | 0.0433 | 0.0433 | 0.0440 | 0.0453 | 0.0463 | 0.0464 | 0.0466 | 0.0469 | 0.0483 | 0.0484 | 0.0492 |
| GSEA | 0.291 | 0.9327 | 0.0598 | 0.1691 | 0.7956 | 0.1772 | 0.0900 | 0.5780 | 0.4619 | 0.4133 | 0.2218 | 0.0718 | 0.5468 | 0.0696 | 0.8420 | 0.3342 | 0.5169 | 0.1087 | 0.3947 | 0.7628 | 0.5228 | 0.5824 | 0.7770 | 0.1379 | 0.0698 | 0.1412 | 0.1897 | 0.0973 | 0.4608 | 0.1388 | 0.2127 | 0.2207 | 0.7351 | 0.1453 | 0.4514 | 0.4100 | 0.1710 | 0.1416 | 0.0612 | 0.5963 | 0.5058 | 0.1657 | 0.1718 | 0.1178 | 0.9480 | 0.1467 | 0.1546 | 0.1377 | 0.0933 | 0.1770 | 0.7882 | 0.6031 | 0.5332 | 0.605 | 0.3370 | 0.6280 | 0.2602 | 0.6960 | 0.3417 | 0.2365 | 0.7404 | 0.1219 | 0.1604 | 0.5501 | 0.4547 | 0.4536 | 0.1674 | 0.1073 | 0.6393 | 0.6722 | 0.5114 | 0.3243 | 0.3485 | 0.1028 | 0.6909 | 0.4692 | 0.2258 | 0.2039 | 0.5153 | 0.1194 | 0.3925 | 0.2875 | 0.0842 | 0.3022 | 0.7105 | 0.1241 | 0.3388 | 0.2717 | 0.2867 |
Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS | BIOCARTA_BAD_PATHWAY | REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION | WINNEPENNINCKX_MELANOMA_METASTASIS_DN | BIOCARTA_CSK_PATHWAY | VERRECCHIA_RESPONSE_TO_TGFB1_C1 | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN | QI_HYPOXIA | WINTER_HYPOXIA_METAGENE | BROWNE_HCMV_INFECTION_2HR_DN | KARLSSON_TGFB1_TARGETS_UP | SEIDEN_ONCOGENESIS_BY_MET | ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 | SEMENZA_HIF1_TARGETS | DAZARD_UV_RESPONSE_CLUSTER_G1 | LANDIS_BREAST_CANCER_PROGRESSION_UP | ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN | MENSE_HYPOXIA_UP | KIM_WT1_TARGETS_12HR_DN | TOOKER_GEMCITABINE_RESISTANCE_DN | REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS | SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM | YANG_BREAST_CANCER_ESR1_LASER_DN | KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3 | KRIEG_HYPOXIA_NOT_VIA_KDM3A | ELVIDGE_HYPOXIA_BY_DMOG_UP | WINTER_HYPOXIA_UP | RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP | CHEN_LUNG_CANCER_SURVIVAL | SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE | PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2 | BHATTACHARYA_EMBRYONIC_STEM_CELL | BIOCARTA_VEGF_PATHWAY | PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN | LEE_DIFFERENTIATING_T_LYMPHOCYTE | REACTOME_PLC_BETA_MEDIATED_EVENTS | REACTOME_OPIOID_SIGNALLING | BIOCARTA_IL12_PATHWAY | KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS | BERENJENO_TRANSFORMED_BY_RHOA_UP | REACTOME_AQUAPORIN_MEDIATED_TRANSPORT | BIOCARTA_HCMV_PATHWAY | CHIN_BREAST_CANCER_COPY_NUMBER_UP | HARRIS_HYPOXIA | YU_MYC_TARGETS_DN | REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS | REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE | FURUKAWA_DUSP6_TARGETS_PCI35_DN | WINTER_HYPOXIA_DN | KEGG_CHRONIC_MYELOID_LEUKEMIA | PID_TCR_PATHWAY | VECCHI_GASTRIC_CANCER_EARLY_UP | RAMALHO_STEMNESS_UP | REACTOME_TRNA_AMINOACYLATION | PRAMOONJAGO_SOX4_TARGETS_UP | SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 | SENESE_HDAC2_TARGETS_UP | KEGG_BLADDER_CANCER | SCHUHMACHER_MYC_TARGETS_UP | KEGG_AMINOACYL_TRNA_BIOSYNTHESIS | REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1 | REACTOME_DAG_AND_IP3_SIGNALING | IVANOVSKA_MIR106B_TARGETS | BIOCARTA_RAS_PATHWAY | SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP | CROMER_METASTASIS_DN | AMIT_EGF_RESPONSE_480_MCF10A | MURAKAMI_UV_RESPONSE_6HR_UP | LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP | LU_EZH2_TARGETS_DN | SESTO_RESPONSE_TO_UV_C2 | MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN | BIOCARTA_CXCR4_PATHWAY | BILD_MYC_ONCOGENIC_SIGNATURE | SMID_BREAST_CANCER_NORMAL_LIKE_UP | LEE_CALORIE_RESTRICTION_NEOCORTEX_DN | REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS | LEONARD_HYPOXIA | COLLER_MYC_TARGETS_UP | BIOCARTA_MTOR_PATHWAY | KEGG_TASTE_TRANSDUCTION | SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP | KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN | GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN | SENESE_HDAC1_TARGETS_UP | SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN | ELVIDGE_HIF1A_TARGETS_DN | NAKAMURA_CANCER_MICROENVIRONMENT_DN | PID_DELTA_NP63_PATHWAY | BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN | REACTOME_IL1_SIGNALING | SWEET_KRAS_ONCOGENIC_SIGNATURE | ELVIDGE_HYPOXIA_UP | MANALO_HYPOXIA_UP | WILLERT_WNT_SIGNALING | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 | LIAO_METASTASIS | BLUM_RESPONSE_TO_SALIRASIB_UP | AMIT_EGF_RESPONSE_480_HELA | BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN | GROSS_HYPOXIA_VIA_ELK3_DN | KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION | BASAKI_YBX1_TARGETS_UP | REACTOME_CA_DEPENDENT_EVENTS | WANG_SMARCE1_TARGETS_DN | SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN | WEI_MYCN_TARGETS_WITH_E_BOX | PID_A6B1_A6B4_INTEGRIN_PATHWAY | STARK_HYPPOCAMPUS_22Q11_DELETION_UP | GENTILE_RESPONSE_CLUSTER_D3 | PID_MTOR_4PATHWAY | DANG_REGULATED_BY_MYC_UP | LI_AMPLIFIED_IN_LUNG_CANCER | LEI_MYB_TARGETS | REACTOME_METABOLISM_OF_NUCLEOTIDES | BIOCARTA_RACCYCD_PATHWAY | SMID_BREAST_CANCER_BASAL_UP | COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP | SMITH_TERT_TARGETS_UP | ALONSO_METASTASIS_EMT_UP | GRANDVAUX_IRF3_TARGETS_DN | KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM | REACTOME_PI_METABOLISM | ZHAN_MULTIPLE_MYELOMA_CD2_DN | CAFFAREL_RESPONSE_TO_THC_24HR_5_UP | NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON | SMIRNOV_RESPONSE_TO_IR_2HR_DN | KEGG_ERBB_SIGNALING_PATHWAY | ZUCCHI_METASTASIS_DN | ZHOU_TNF_SIGNALING_30MIN | PID_TAP63_PATHWAY | KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN | REACTOME_PYRIMIDINE_METABOLISM | NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN | HOFMANN_CELL_LYMPHOMA_UP | BIOCARTA_FMLP_PATHWAY | PID_MYC_ACTIV_PATHWAY | CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN | MOOTHA_GLUCONEOGENESIS | PID_EPHB_FWD_PATHWAY | KIM_WT1_TARGETS_8HR_UP | PID_UPA_UPAR_PATHWAY | SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS | FARMER_BREAST_CANCER_BASAL_VS_LULMINAL | BHAT_ESR1_TARGETS_VIA_AKT1_UP | SHEPARD_CRUSH_AND_BURN_MUTANT_UP | NUYTTEN_NIPP1_TARGETS_UP | DOANE_BREAST_CANCER_CLASSES_DN | SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE | CLIMENT_BREAST_CANCER_COPY_NUMBER_UP | THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP | SANA_RESPONSE_TO_IFNG_DN | KEGG_PYRIMIDINE_METABOLISM | KIM_WT1_TARGETS_UP | ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF | FRIDMAN_IMMORTALIZATION_DN | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 | ZHAN_MULTIPLE_MYELOMA_PR_UP | PHONG_TNF_RESPONSE_VIA_P38_PARTIAL | BIOCARTA_SPPA_PATHWAY | JIANG_HYPOXIA_NORMAL | WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN | DAZARD_UV_RESPONSE_CLUSTER_G2 | RICKMAN_HEAD_AND_NECK_CANCER_D | CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN | PID_CD8_TCR_PATHWAY | GENTILE_UV_RESPONSE_CLUSTER_D5 | BILD_HRAS_ONCOGENIC_SIGNATURE | LIM_MAMMARY_STEM_CELL_DN | DITTMER_PTHLH_TARGETS_UP | LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT | WHITFIELD_CELL_CYCLE_G2_M | POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP | PID_NCADHERIN_PATHWAY | GENTILE_UV_RESPONSE_CLUSTER_D7 | PID_HIF1_TFPATHWAY | NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GROSS_HYPOXIA_VIA_ELK3_ONLY_UP | NEMETH_INFLAMMATORY_RESPONSE_LPS_UP | LINDGREN_BLADDER_CANCER_CLUSTER_3_DN | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP | NUYTTEN_NIPP1_TARGETS_DN | SENESE_HDAC3_TARGETS_UP | MORI_SMALL_PRE_BII_LYMPHOCYTE_DN | PID_CERAMIDE_PATHWAY | DORSAM_HOXA9_TARGETS_UP | NATSUME_RESPONSE_TO_INTERFERON_BETA_DN | WANG_LMO4_TARGETS_DN | MOHANKUMAR_HOXA1_TARGETS_DN | ONDER_CDH1_TARGETS_1_DN | BENPORATH_MYC_TARGETS_WITH_EBOX | FERNANDEZ_BOUND_BY_MYC | GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN | KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP | YAGI_AML_WITH_INV_16_TRANSLOCATION | FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP | LINSLEY_MIR16_TARGETS | KEGG_ACUTE_MYELOID_LEUKEMIA | HOELZEL_NF1_TARGETS_UP | BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP | KEGG_PATHWAYS_IN_CANCER | BASSO_HAIRY_CELL_LEUKEMIA_UP | REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS | GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN | BRUINS_UVC_RESPONSE_LATE | MARTINEZ_RB1_TARGETS_UP | DOUGLAS_BMI1_TARGETS_UP | ALFANO_MYC_TARGETS | RAMALHO_STEMNESS_DN | VANASSE_BCL2_TARGETS_DN | REACTOME_DARPP_32_EVENTS | CHANG_CORE_SERUM_RESPONSE_DN | ST_G_ALPHA_I_PATHWAY | REACTOME_RECYCLING_PATHWAY_OF_L1 | WILENSKY_RESPONSE_TO_DARAPLADIB | BORCZUK_MALIGNANT_MESOTHELIOMA_DN | BIOCARTA_IL7_PATHWAY | REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION | REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP | PID_RAC1_REG_PATHWAY | MIKKELSEN_IPS_WITH_HCP_H3K27ME3 | ZHAN_MULTIPLE_MYELOMA_CD2_UP | ROVERSI_GLIOMA_COPY_NUMBER_UP | SCHLOSSER_SERUM_RESPONSE_UP | FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP | MIKKELSEN_IPS_ICP_WITH_H3K27ME3 | REACTOME_G_PROTEIN_ACTIVATION | REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS | CORRE_MULTIPLE_MYELOMA_DN | REACTOME_GLYCOSPHINGOLIPID_METABOLISM | BIOCARTA_CTLA4_PATHWAY | VECCHI_GASTRIC_CANCER_EARLY_DN | REACTOME_INTEGRATION_OF_ENERGY_METABOLISM | AKL_HTLV1_INFECTION_DN | KATSANOU_ELAVL1_TARGETS_UP | VALK_AML_WITH_FLT3_ITD | LEIN_MIDBRAIN_MARKERS | HUTTMANN_B_CLL_POOR_SURVIVAL_UP | KEGG_GNRH_SIGNALING_PATHWAY | LEE_LIVER_CANCER_SURVIVAL_UP | LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES | KEGG_MELANOGENESIS | MA_MYELOID_DIFFERENTIATION_DN | REACTOME_REGULATION_OF_INSULIN_SECRETION | HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP | GRADE_COLON_AND_RECTAL_CANCER_DN | ST_ADRENERGIC | CROMER_TUMORIGENESIS_DN | PID_IL3_PATHWAY | REACTOME_G_ALPHA_S_SIGNALLING_EVENTS | CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY | MCCLUNG_COCAINE_REWARD_5D | REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR | ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION | MCCLUNG_DELTA_FOSB_TARGETS_8WK | NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN | KONDO_PROSTATE_CANCER_WITH_H3K27ME3 | SANSOM_APC_TARGETS_DN | WNT_SIGNALING | KASLER_HDAC7_TARGETS_1_UP | REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY | KEGG_GLYCEROPHOSPHOLIPID_METABOLISM | PEREZ_TP53_TARGETS | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP | PEREZ_TP63_TARGETS | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.7378 | 0.5571 | 0.5781 | 0.2336 | 0.2743 | 0.3037 | 0.0761 | 0.0997 | 0.2149 | 0.0750 | 0.1620 | 0.8947 | 0.1020 | 0.0891 | 0.1534 | 0.3641 | 0.2668 | 0.1856 | 0.9176 | 0.6607 | 0.1265 | 0.286 | 0.5220 | 0.2893 | 0.268 | 0.2695 | 0.0564 | 0.4625 | 0.1741 | 0.2944 | 0.2293 | 0.2315 | 0.3597 | 0.1862 | 0.6008 | 0.6931 | 0.6419 | 0.0542 | 0.4035 | 0.0515 | 0.7286 | 0.0759 | 0.0579 | 0.3090 | 0.1584 | 0.7365 | 0.7886 | 0.0714 | 0.0723 | 0.8479 | 0.5169 | 0.2884 | 0.5786 | 0.8943 | 0.2648 | 0.4949 | 0.1011 | 0.0972 | 0.1694 | 0.8929 | 0.5817 | 0.7332 | 0.4657 | 0.8005 | 0.1148 | 0.2231 | 0.9986 | 0.2554 | 0.7102 | 0.5615 | 0.2025 | 0.5714 | 0.4260 | 0.9997 | 0.1820 | 0.8684 | 0.8024 | 0.4020 | 0.8034 | 0.1146 | 0.9698 | 0.9356 | 0.1459 | 0.9933 | 0.6897 | 0.7546 | 0.3694 | 0.2905 | 0.8757 | 0.2959 | 0.9911 | 0.3079 | 0.1854 | 0.3089 | 0.1144 | 0.9810 | 0.8755 | 0.9731 | 0.2279 | 0.4236 | 0.8676 | 0.2433 | 0.5499 | 0.7948 | 0.0868 | 0.1761 | 0.9459 | 0.2861 | 0.2832 | 0.3370 | 0.6310 | 0.2453 | 0.0709 | 0.0737 | 0.3087 | 0.6667 | 0.1466 | 0.1469 | 0.9065 | 0.3790 | 0.5266 | 0.8446 | 0.6033 | 0.0636 | 0.8586 | 0.2948 | 0.9103 | 0.1354 | 0.0613 | 0.4811 | 0.2623 | 0.6438 | 0.3242 | 0.0508 | 0.2102 | 0.7541 | 0.1961 | 0.6169 | 0.0562 | 0.8022 | 0.5121 | 0.6111 | 0.1176 | 0.2852 | 0.8856 | 0.9848 | 0.8985 | 0.1861 | 0.1331 | 0.1062 | 0.3902 | 0.1575 | 0.3426 | 0.7689 | 0.6075 | 0.4671 | 0.8618 | 0.3905 | 0.6833 | 0.6805 | 0.3967 | 0.4568 | 0.2503 | 0.2012 | 0.1441 | 0.8961 | 0.1235 | 0.8780 | 0.1719 | 0.0819 | 0.0728 | 0.9807 | 0.0526 | 0.5686 | 0.7035 | 0.2372 | 0.7971 | 0.5284 | 0.722 | 0.5458 | 0.3099 | 0.8987 | 0.1661 | 0.3209 | 0.5076 | 0.8819 | 0.7034 | 0.2284 | 0.9657 | 0.2203 | 0.7544 | 0.2850 | 0.0736 | 0.2230 | 0.6301 | 0.5829 | 0.7445 | 0.8445 | 0.3102 | 0.1377 | 0.8461 | 0.5774 | 0.7244 | 0.8964 | 0.0827 | 0.9957 | 0.9254 | 0.9651 | 0.6121 | 0.7684 | 0.9926 | 0.7093 | 0.7984 | 0.5049 | 0.2448 | 0.2112 | 0.8308 | 0.0510 | 0.2913 | 0.6929 | 0.9865 | 0.7825 | 0.7982 | 0.5034 | 0.2603 | 0.1376 | 0.3350 | 0.8724 | 0.7865 | 0.5926 | 0.8722 | 0.7125 | 0.3439 | 0.5457 | 0.5283 | 0.605 | 0.2805 | 0.9854 | 0.1286 | 0.8252 | 0.6748 | 0.8479 | 0.0555 | 0.7670 | 0.9271 | 0.4653 | 0.3027 | 0.9999 | 0.3101 | 0.0970 | 0.8599 | 0.8667 | 0.3382 | 0.0967 | 0.8227 | 0.6332 | 0.6905 | 0.7165 | 0.9925 | 0.3234 | 0.9817 | 0.5284 | 0.3226 | 0.1146 | 0.9212 | 0.2590 | 0.9993 |
| GSEA | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0024 | 0.0000 | 0.0000 | 0.0045 | 0.0021 | 0.0000 | 0.0047 | 0.0000 | 0.0021 | 0.0066 | 0.0046 | 0.0042 | 0.0021 | 0.0021 | 0.0021 | 0.008 | 0.0023 | 0.0023 | 0.000 | 0.0022 | 0.0000 | 0.0020 | 0.0069 | 0.0022 | 0.0098 | 0.0041 | 0.0000 | 0.0000 | 0.0095 | 0.0000 | 0.0000 | 0.0130 | 0.0084 | 0.0150 | 0.0018 | 0.0041 | 0.0115 | 0.0114 | 0.0098 | 0.0000 | 0.0018 | 0.0261 | 0.0060 | 0.0041 | 0.0000 | 0.0188 | 0.0140 | 0.0308 | 0.0150 | 0.0465 | 0.0092 | 0.0093 | 0.0267 | 0.0308 | 0.0052 | 0.0000 | 0.0174 | 0.0085 | 0.0262 | 0.0193 | 0.0116 | 0.0128 | 0.0203 | 0.0130 | 0.0142 | 0.0217 | 0.0221 | 0.0067 | 0.0167 | 0.0023 | 0.0073 | 0.0247 | 0.0251 | 0.0098 | 0.0034 | 0.0123 | 0.0020 | 0.0161 | 0.0023 | 0.0229 | 0.0114 | 0.0394 | 0.0046 | 0.0249 | 0.0130 | 0.0232 | 0.0112 | 0.0088 | 0.0100 | 0.0182 | 0.0113 | 0.0087 | 0.0211 | 0.0104 | 0.0118 | 0.0072 | 0.0196 | 0.0018 | 0.0047 | 0.0397 | 0.0131 | 0.0147 | 0.0018 | 0.0343 | 0.0165 | 0.0269 | 0.0172 | 0.0022 | 0.0147 | 0.0263 | 0.0026 | 0.0183 | 0.0288 | 0.0466 | 0.0346 | 0.0444 | 0.0251 | 0.0341 | 0.0424 | 0.0363 | 0.0263 | 0.0044 | 0.0398 | 0.0286 | 0.0292 | 0.0219 | 0.0199 | 0.0141 | 0.0221 | 0.0305 | 0.0375 | 0.0335 | 0.0309 | 0.0198 | 0.0252 | 0.0355 | 0.0432 | 0.0000 | 0.0024 | 0.0179 | 0.0117 | 0.0381 | 0.0165 | 0.0252 | 0.0303 | 0.0438 | 0.0437 | 0.0279 | 0.0435 | 0.0461 | 0.0219 | 0.0420 | 0.0376 | 0.0291 | 0.0129 | 0.0345 | 0.0424 | 0.0067 | 0.0345 | 0.0144 | 0.0365 | 0.0273 | 0.0459 | 0.0455 | 0.0412 | 0.0462 | 0.0053 | 0.0390 | 0.0428 | 0.0402 | 0.0279 | 0.0420 | 0.044 | 0.0254 | 0.0330 | 0.0168 | 0.0291 | 0.0203 | 0.0488 | 0.0473 | 0.0337 | 0.0499 | 0.0327 | 0.0341 | 0.0340 | 0.0162 | 0.0164 | 0.0115 | 0.0218 | 0.0205 | 0.0480 | 0.0396 | 0.0465 | 0.0482 | 0.0477 | 0.0302 | 0.0394 | 0.0071 | 0.0350 | 0.0383 | 0.0134 | 0.0467 | 0.0477 | 0.0128 | 0.0035 | 0.0096 | 0.0167 | 0.0053 | 0.0196 | 0.0251 | 0.0181 | 0.0366 | 0.0190 | 0.0346 | 0.0176 | 0.0378 | 0.0252 | 0.0401 | 0.0368 | 0.0187 | 0.0245 | 0.0251 | 0.0297 | 0.0343 | 0.0137 | 0.0443 | 0.0462 | 0.0370 | 0.0283 | 0.049 | 0.0486 | 0.0491 | 0.0433 | 0.0468 | 0.0394 | 0.0334 | 0.0399 | 0.0304 | 0.0455 | 0.0407 | 0.0323 | 0.0383 | 0.0455 | 0.0433 | 0.0478 | 0.0411 | 0.0414 | 0.0243 | 0.0396 | 0.0491 | 0.0322 | 0.0444 | 0.0291 | 0.0337 | 0.0255 | 0.0255 | 0.0407 | 0.0360 | 0.0162 | 0.0349 | 0.0339 |
# stopCluster(cl)
library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw())
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ABE_VEGFA_TARGETS_2HR"
## [1] "ABE_VEGFA_TARGETS_30MIN"
## [1] "ANDERSEN_LIVER_CANCER_KRT19_UP"
## [1] "APPIERTO_RESPONSE_TO_FENRETINIDE_DN"
## [1] "BENPORATH_PROLIFERATION"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN"
## [1] "BOYLAN_MULTIPLE_MYELOMA_D_DN"
## [1] "BOYLAN_MULTIPLE_MYELOMA_PCA1_UP"
## [1] "BROWNE_HCMV_INFECTION_2HR_UP"
## [1] "CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP"
## [1] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP"
## [1] "CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN"
## [1] "DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN"
## [1] "DELPUECH_FOXO3_TARGETS_UP"
## [1] "DOANE_RESPONSE_TO_ANDROGEN_UP"
## [1] "DORN_ADENOVIRUS_INFECTION_12HR_UP"
## [1] "DORN_ADENOVIRUS_INFECTION_48HR_DN"
## [1] "DORSAM_HOXA9_TARGETS_DN"
## [1] "DURAND_STROMA_NS_UP"
## [1] "GALLUZZI_PERMEABILIZE_MITOCHONDRIA"
## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP"
## [1] "HAHTOLA_SEZARY_SYNDROM_UP"
## [1] "HAN_JNK_SINGALING_UP"
## [1] "HELLER_SILENCED_BY_METHYLATION_UP"
## [1] "HENDRICKS_SMARCA4_TARGETS_UP"
## [1] "HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN"
## [1] "HUPER_BREAST_BASAL_VS_LUMINAL_UP"
## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP"
## [1] "JIANG_AGING_CEREBRAL_CORTEX_DN"
## [1] "JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP"
## [1] "KAAB_FAILED_HEART_VENTRICLE_DN"
## [1] "KAMIKUBO_MYELOID_CEBPA_NETWORK"
## [1] "KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"
## [1] "KEGG_PROPANOATE_METABOLISM"
## [1] "KEGG_PYRUVATE_METABOLISM"
## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"
## [1] "KIM_TIAL1_TARGETS"
## [1] "KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP"
## [1] "KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP"
## [1] "LEE_TARGETS_OF_PTCH1_AND_SUFU_DN"
## [1] "LINDVALL_IMMORTALIZED_BY_TERT_UP"
## [1] "MALONEY_RESPONSE_TO_17AAG_DN"
## [1] "MCDOWELL_ACUTE_LUNG_INJURY_UP"
## [1] "MEISSNER_BRAIN_HCP_WITH_H3K27ME3"
## [1] "MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED"
## [1] "MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED"
## [1] "MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP"
## [1] "MOREIRA_RESPONSE_TO_TSA_UP"
## [1] "MUELLER_METHYLATED_IN_GLIOBLASTOMA"
## [1] "NABA_MATRISOME_ASSOCIATED"
## [1] "NABA_SECRETED_FACTORS"
## [1] "NAKAJIMA_EOSINOPHIL"
## [1] "OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP"
## [1] "PAL_PRMT5_TARGETS_DN"
## [1] "PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP"
## [1] "PARK_APL_PATHOGENESIS_DN"
## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP"
## [1] "REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION"
## [1] "REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING"
## [1] "REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE"
## [1] "ROSS_AML_WITH_PML_RARA_FUSION"
## [1] "SANA_TNF_SIGNALING_DN"
## [1] "SANSOM_APC_TARGETS_UP"
## [1] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"
## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN"
## [1] "SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1"
## [1] "SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5"
## [1] "SIMBULAN_UV_RESPONSE_NORMAL_DN"
## [1] "SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN"
## [1] "STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN"
## [1] "STEARMAN_TUMOR_FIELD_EFFECT_UP"
## [1] "STEIN_ESR1_TARGETS"
## [1] "STEIN_ESRRA_TARGETS"
## [1] "SU_PLACENTA"
## [1] "SWEET_LUNG_CANCER_KRAS_UP"
## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN"
## [1] "TSUNODA_CISPLATIN_RESISTANCE_DN"
## [1] "VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN"
## [1] "VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP"
## [1] "VANTVEER_BREAST_CANCER_METASTASIS_UP"
## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN"
## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP"
## [1] "WANG_BARRETTS_ESOPHAGUS_UP"
## [1] "YAMAZAKI_TCEB3_TARGETS_DN"
## [1] "YANAGIHARA_ESX1_TARGETS"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"
## [1] "ZAMORA_NOS2_TARGETS_UP"
## [1] "ZHAN_MULTIPLE_MYELOMA_DN"
## [1] "ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN"
rownames(gsea_results_significant)
## [1] "REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS"
## [2] "BIOCARTA_BAD_PATHWAY"
## [3] "REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION"
## [4] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"
## [5] "BIOCARTA_CSK_PATHWAY"
## [6] "VERRECCHIA_RESPONSE_TO_TGFB1_C1"
## [7] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN"
## [8] "QI_HYPOXIA"
## [9] "WINTER_HYPOXIA_METAGENE"
## [10] "LI_LUNG_CANCER"
## [11] "BROWNE_HCMV_INFECTION_2HR_DN"
## [12] "KARLSSON_TGFB1_TARGETS_UP"
## [13] "SEIDEN_ONCOGENESIS_BY_MET"
## [14] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"
## [15] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN"
## [16] "SEMENZA_HIF1_TARGETS"
## [17] "DAZARD_UV_RESPONSE_CLUSTER_G1"
## [18] "GU_PDEF_TARGETS_DN"
## [19] "LANDIS_BREAST_CANCER_PROGRESSION_UP"
## [20] "ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN"
## [21] "MENSE_HYPOXIA_UP"
## [22] "KIM_WT1_TARGETS_12HR_DN"
## [23] "TOOKER_GEMCITABINE_RESISTANCE_DN"
## [24] "ENK_UV_RESPONSE_EPIDERMIS_UP"
## [25] "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS"
## [26] "SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM"
## [27] "YANG_BREAST_CANCER_ESR1_LASER_DN"
## [28] "KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3"
## [29] "KRIEG_HYPOXIA_NOT_VIA_KDM3A"
## [30] "ELVIDGE_HYPOXIA_BY_DMOG_UP"
## [31] "WINTER_HYPOXIA_UP"
## [32] "RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP"
## [33] "CHEN_LUNG_CANCER_SURVIVAL"
## [34] "KEGG_GLYCOLYSIS_GLUCONEOGENESIS"
## [35] "SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE"
## [36] "PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2"
## [37] "BHATTACHARYA_EMBRYONIC_STEM_CELL"
## [38] "BIOCARTA_VEGF_PATHWAY"
## [39] "MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP"
## [40] "HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP"
## [41] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"
## [42] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"
## [43] "REACTOME_PLC_BETA_MEDIATED_EVENTS"
## [44] "REACTOME_OPIOID_SIGNALLING"
## [45] "BIOCARTA_IL12_PATHWAY"
## [46] "KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
## [47] "BERENJENO_TRANSFORMED_BY_RHOA_UP"
## [48] "REACTOME_AQUAPORIN_MEDIATED_TRANSPORT"
## [49] "BIOCARTA_HCMV_PATHWAY"
## [50] "CHIN_BREAST_CANCER_COPY_NUMBER_UP"
## [51] "HARRIS_HYPOXIA"
## [52] "YU_MYC_TARGETS_DN"
## [53] "REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS"
## [54] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"
## [55] "FURUKAWA_DUSP6_TARGETS_PCI35_DN"
## [56] "WINTER_HYPOXIA_DN"
## [57] "KEGG_CHRONIC_MYELOID_LEUKEMIA"
## [58] "PID_TCR_PATHWAY"
## [59] "VECCHI_GASTRIC_CANCER_EARLY_UP"
## [60] "RAMALHO_STEMNESS_UP"
## [61] "REACTOME_TRNA_AMINOACYLATION"
## [62] "PRAMOONJAGO_SOX4_TARGETS_UP"
## [63] "SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6"
## [64] "SENESE_HDAC2_TARGETS_UP"
## [65] "KEGG_BLADDER_CANCER"
## [66] "SCHUHMACHER_MYC_TARGETS_UP"
## [67] "KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
## [68] "REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1"
## [69] "REACTOME_DAG_AND_IP3_SIGNALING"
## [70] "IVANOVSKA_MIR106B_TARGETS"
## [71] "KIM_HYPOXIA"
## [72] "BIOCARTA_RAS_PATHWAY"
## [73] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP"
## [74] "CROMER_METASTASIS_DN"
## [75] "AMIT_EGF_RESPONSE_480_MCF10A"
## [76] "MURAKAMI_UV_RESPONSE_6HR_UP"
## [77] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"
## [78] "LU_EZH2_TARGETS_DN"
## [79] "SESTO_RESPONSE_TO_UV_C2"
## [80] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN"
## [81] "BIOCARTA_CXCR4_PATHWAY"
## [82] "BILD_MYC_ONCOGENIC_SIGNATURE"
## [83] "GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN"
## [84] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"
## [85] "LEE_CALORIE_RESTRICTION_NEOCORTEX_DN"
## [86] "REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS"
## [87] "LEONARD_HYPOXIA"
## [88] "COLLER_MYC_TARGETS_UP"
## [89] "BIOCARTA_MTOR_PATHWAY"
## [90] "KEGG_TASTE_TRANSDUCTION"
## [91] "JAEGER_METASTASIS_DN"
## [92] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP"
## [93] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"
## [94] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN"
## [95] "SENESE_HDAC1_TARGETS_UP"
## [96] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"
## [97] "ELVIDGE_HIF1A_TARGETS_DN"
## [98] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP"
## [99] "NAKAMURA_CANCER_MICROENVIRONMENT_DN"
## [100] "PID_DELTA_NP63_PATHWAY"
## [101] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"
## [102] "COLDREN_GEFITINIB_RESISTANCE_DN"
## [103] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"
## [104] "REACTOME_IL1_SIGNALING"
## [105] "SWEET_KRAS_ONCOGENIC_SIGNATURE"
## [106] "ELVIDGE_HYPOXIA_UP"
## [107] "MANALO_HYPOXIA_UP"
## [108] "BIOCARTA_CERAMIDE_PATHWAY"
## [109] "WILLERT_WNT_SIGNALING"
## [110] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4"
## [111] "LIAO_METASTASIS"
## [112] "BLUM_RESPONSE_TO_SALIRASIB_UP"
## [113] "AMIT_EGF_RESPONSE_480_HELA"
## [114] "BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN"
## [115] "VANTVEER_BREAST_CANCER_ESR1_DN"
## [116] "GROSS_HYPOXIA_VIA_ELK3_DN"
## [117] "KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
## [118] "BASAKI_YBX1_TARGETS_UP"
## [119] "REACTOME_CA_DEPENDENT_EVENTS"
## [120] "WANG_SMARCE1_TARGETS_DN"
## [121] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN"
## [122] "WEI_MYCN_TARGETS_WITH_E_BOX"
## [123] "PID_A6B1_A6B4_INTEGRIN_PATHWAY"
## [124] "WU_CELL_MIGRATION"
## [125] "STARK_HYPPOCAMPUS_22Q11_DELETION_UP"
## [126] "GENTILE_RESPONSE_CLUSTER_D3"
## [127] "PID_MTOR_4PATHWAY"
## [128] "AMIT_SERUM_RESPONSE_480_MCF10A"
## [129] "HUPER_BREAST_BASAL_VS_LUMINAL_DN"
## [130] "DANG_REGULATED_BY_MYC_UP"
## [131] "LI_AMPLIFIED_IN_LUNG_CANCER"
## [132] "LEI_MYB_TARGETS"
## [133] "REACTOME_METABOLISM_OF_NUCLEOTIDES"
## [134] "BIOCARTA_RACCYCD_PATHWAY"
## [135] "SESTO_RESPONSE_TO_UV_C1"
## [136] "SMID_BREAST_CANCER_BASAL_UP"
## [137] "COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP"
## [138] "SMITH_TERT_TARGETS_UP"
## [139] "ALONSO_METASTASIS_EMT_UP"
## [140] "GRANDVAUX_IRF3_TARGETS_DN"
## [141] "KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
## [142] "REACTOME_PI_METABOLISM"
## [143] "ZHAN_MULTIPLE_MYELOMA_CD2_DN"
## [144] "CAFFAREL_RESPONSE_TO_THC_24HR_5_UP"
## [145] "SABATES_COLORECTAL_ADENOMA_UP"
## [146] "NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON"
## [147] "SMIRNOV_RESPONSE_TO_IR_2HR_DN"
## [148] "KEGG_ERBB_SIGNALING_PATHWAY"
## [149] "ZUCCHI_METASTASIS_DN"
## [150] "ZHOU_TNF_SIGNALING_30MIN"
## [151] "PID_TAP63_PATHWAY"
## [152] "KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN"
## [153] "REACTOME_PYRIMIDINE_METABOLISM"
## [154] "NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN"
## [155] "HOFMANN_CELL_LYMPHOMA_UP"
## [156] "BIOCARTA_FMLP_PATHWAY"
## [157] "PID_MYC_ACTIV_PATHWAY"
## [158] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"
## [159] "CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN"
## [160] "MOOTHA_GLUCONEOGENESIS"
## [161] "PID_EPHB_FWD_PATHWAY"
## [162] "KIM_WT1_TARGETS_8HR_UP"
## [163] "PID_UPA_UPAR_PATHWAY"
## [164] "SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS"
## [165] "HAHTOLA_CTCL_CUTANEOUS"
## [166] "FARMER_BREAST_CANCER_BASAL_VS_LULMINAL"
## [167] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"
## [168] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"
## [169] "NUYTTEN_NIPP1_TARGETS_UP"
## [170] "BAE_BRCA1_TARGETS_UP"
## [171] "DOANE_BREAST_CANCER_CLASSES_DN"
## [172] "SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE"
## [173] "CLIMENT_BREAST_CANCER_COPY_NUMBER_UP"
## [174] "THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP"
## [175] "SANA_RESPONSE_TO_IFNG_DN"
## [176] "KEGG_PYRIMIDINE_METABOLISM"
## [177] "KIM_WT1_TARGETS_UP"
## [178] "ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF"
## [179] "FRIDMAN_IMMORTALIZATION_DN"
## [180] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"
## [181] "ZHAN_MULTIPLE_MYELOMA_PR_UP"
## [182] "PHONG_TNF_RESPONSE_VIA_P38_PARTIAL"
## [183] "BIOCARTA_SPPA_PATHWAY"
## [184] "JIANG_HYPOXIA_NORMAL"
## [185] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN"
## [186] "DAZARD_UV_RESPONSE_CLUSTER_G2"
## [187] "RICKMAN_HEAD_AND_NECK_CANCER_D"
## [188] "CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN"
## [189] "PID_CD8_TCR_PATHWAY"
## [190] "GENTILE_UV_RESPONSE_CLUSTER_D5"
## [191] "BILD_HRAS_ONCOGENIC_SIGNATURE"
## [192] "LIM_MAMMARY_STEM_CELL_DN"
## [193] "DITTMER_PTHLH_TARGETS_UP"
## [194] "WOOD_EBV_EBNA1_TARGETS_DN"
## [195] "LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT"
## [196] "WHITFIELD_CELL_CYCLE_G2_M"
## [197] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP"
## [198] "PID_NCADHERIN_PATHWAY"
## [199] "GENTILE_UV_RESPONSE_CLUSTER_D7"
## [200] "PID_HIF1_TFPATHWAY"
## [201] "ONDER_CDH1_TARGETS_2_DN"
## [202] "NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP"
## [203] "GROSS_HYPOXIA_VIA_ELK3_ONLY_UP"
## [204] "NEMETH_INFLAMMATORY_RESPONSE_LPS_UP"
## [205] "LINDGREN_BLADDER_CANCER_CLUSTER_3_DN"
## [206] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP"
## [207] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP"
## [208] "NUYTTEN_NIPP1_TARGETS_DN"
## [209] "SENESE_HDAC3_TARGETS_UP"
## [210] "MORI_SMALL_PRE_BII_LYMPHOCYTE_DN"
## [211] "PID_CERAMIDE_PATHWAY"
## [212] "DORSAM_HOXA9_TARGETS_UP"
## [213] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"
## [214] "LEE_LIVER_CANCER_ACOX1_UP"
## [215] "WANG_LMO4_TARGETS_DN"
## [216] "MOHANKUMAR_HOXA1_TARGETS_DN"
## [217] "ONDER_CDH1_TARGETS_1_DN"
## [218] "BENPORATH_MYC_TARGETS_WITH_EBOX"
## [219] "FERNANDEZ_BOUND_BY_MYC"
## [220] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"
## [221] "KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP"
## [222] "YAGI_AML_WITH_INV_16_TRANSLOCATION"
## [223] "HAN_SATB1_TARGETS_UP"
## [224] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"
## [225] "LINSLEY_MIR16_TARGETS"
## [226] "KEGG_ACUTE_MYELOID_LEUKEMIA"
## [227] "HOELZEL_NF1_TARGETS_UP"
## [228] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"
## [229] "KEGG_PATHWAYS_IN_CANCER"
## [230] "BASSO_HAIRY_CELL_LEUKEMIA_UP"
## [231] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"
## [232] "GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN"
## [233] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"
## [234] "BRUINS_UVC_RESPONSE_LATE"
## [235] "MARTINEZ_RB1_TARGETS_UP"
## [236] "DOUGLAS_BMI1_TARGETS_UP"
## [237] "ALFANO_MYC_TARGETS"
## [238] "RAMALHO_STEMNESS_DN"
## [239] "VANASSE_BCL2_TARGETS_DN"
## [240] "REACTOME_DARPP_32_EVENTS"
## [241] "CHANG_CORE_SERUM_RESPONSE_DN"
## [242] "ST_G_ALPHA_I_PATHWAY"
## [243] "REACTOME_RECYCLING_PATHWAY_OF_L1"
## [244] "WILENSKY_RESPONSE_TO_DARAPLADIB"
## [245] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"
## [246] "BIOCARTA_IL7_PATHWAY"
## [247] "REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION"
## [248] "REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL"
## [249] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP"
## [250] "PID_RAC1_REG_PATHWAY"
## [251] "MIKKELSEN_IPS_WITH_HCP_H3K27ME3"
## [252] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"
## [253] "ROVERSI_GLIOMA_COPY_NUMBER_UP"
## [254] "JIANG_AGING_HYPOTHALAMUS_DN"
## [255] "SCHLOSSER_SERUM_RESPONSE_UP"
## [256] "FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP"
## [257] "MIKKELSEN_IPS_ICP_WITH_H3K27ME3"
## [258] "REACTOME_G_PROTEIN_ACTIVATION"
## [259] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
## [260] "CORRE_MULTIPLE_MYELOMA_DN"
## [261] "REACTOME_GLYCOSPHINGOLIPID_METABOLISM"
## [262] "BIOCARTA_CTLA4_PATHWAY"
## [263] "VECCHI_GASTRIC_CANCER_EARLY_DN"
## [264] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"
## [265] "AKL_HTLV1_INFECTION_DN"
## [266] "KATSANOU_ELAVL1_TARGETS_UP"
## [267] "VALK_AML_WITH_FLT3_ITD"
## [268] "LEIN_MIDBRAIN_MARKERS"
## [269] "HUTTMANN_B_CLL_POOR_SURVIVAL_UP"
## [270] "KEGG_GNRH_SIGNALING_PATHWAY"
## [271] "LEE_LIVER_CANCER_SURVIVAL_UP"
## [272] "LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES"
## [273] "KEGG_MELANOGENESIS"
## [274] "MA_MYELOID_DIFFERENTIATION_DN"
## [275] "REACTOME_REGULATION_OF_INSULIN_SECRETION"
## [276] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"
## [277] "GRADE_COLON_AND_RECTAL_CANCER_DN"
## [278] "ST_ADRENERGIC"
## [279] "CROMER_TUMORIGENESIS_DN"
## [280] "PID_IL3_PATHWAY"
## [281] "REACTOME_G_ALPHA_S_SIGNALLING_EVENTS"
## [282] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"
## [283] "MCCLUNG_COCAINE_REWARD_5D"
## [284] "REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR"
## [285] "ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION"
## [286] "MCCLUNG_DELTA_FOSB_TARGETS_8WK"
## [287] "NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN"
## [288] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"
## [289] "SANSOM_APC_TARGETS_DN"
## [290] "WNT_SIGNALING"
## [291] "KASLER_HDAC7_TARGETS_1_UP"
## [292] "REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY"
## [293] "KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
## [294] "PEREZ_TP53_TARGETS"
## [295] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP"
## [296] "PEREZ_TP63_TARGETS"
for (name in (Significant_in_GSEA_not_in_dcor)){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS"
## [1] "BIOCARTA_BAD_PATHWAY"
## [1] "REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION"
## [1] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"
## [1] "BIOCARTA_CSK_PATHWAY"
## [1] "VERRECCHIA_RESPONSE_TO_TGFB1_C1"
## [1] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN"
## [1] "QI_HYPOXIA"
## [1] "WINTER_HYPOXIA_METAGENE"
## [1] "BROWNE_HCMV_INFECTION_2HR_DN"
## [1] "KARLSSON_TGFB1_TARGETS_UP"
## [1] "SEIDEN_ONCOGENESIS_BY_MET"
## [1] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"
## [1] "SEMENZA_HIF1_TARGETS"
## [1] "DAZARD_UV_RESPONSE_CLUSTER_G1"
## [1] "LANDIS_BREAST_CANCER_PROGRESSION_UP"
## [1] "ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN"
## [1] "MENSE_HYPOXIA_UP"
## [1] "KIM_WT1_TARGETS_12HR_DN"
## [1] "TOOKER_GEMCITABINE_RESISTANCE_DN"
## [1] "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS"
## [1] "SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM"
## [1] "YANG_BREAST_CANCER_ESR1_LASER_DN"
## [1] "KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3"
## [1] "KRIEG_HYPOXIA_NOT_VIA_KDM3A"
## [1] "ELVIDGE_HYPOXIA_BY_DMOG_UP"
## [1] "WINTER_HYPOXIA_UP"
## [1] "RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP"
## [1] "CHEN_LUNG_CANCER_SURVIVAL"
## [1] "SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE"
## [1] "PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2"
## [1] "BHATTACHARYA_EMBRYONIC_STEM_CELL"
## [1] "BIOCARTA_VEGF_PATHWAY"
## [1] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"
## [1] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"
## [1] "REACTOME_PLC_BETA_MEDIATED_EVENTS"
## [1] "REACTOME_OPIOID_SIGNALLING"
## [1] "BIOCARTA_IL12_PATHWAY"
## [1] "KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
## [1] "BERENJENO_TRANSFORMED_BY_RHOA_UP"
## [1] "REACTOME_AQUAPORIN_MEDIATED_TRANSPORT"
## [1] "BIOCARTA_HCMV_PATHWAY"
## [1] "CHIN_BREAST_CANCER_COPY_NUMBER_UP"
## [1] "HARRIS_HYPOXIA"
## [1] "YU_MYC_TARGETS_DN"
## [1] "REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS"
## [1] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"
## [1] "FURUKAWA_DUSP6_TARGETS_PCI35_DN"
## [1] "WINTER_HYPOXIA_DN"
## [1] "KEGG_CHRONIC_MYELOID_LEUKEMIA"
## [1] "PID_TCR_PATHWAY"
## [1] "VECCHI_GASTRIC_CANCER_EARLY_UP"
## [1] "RAMALHO_STEMNESS_UP"
## [1] "REACTOME_TRNA_AMINOACYLATION"
## [1] "PRAMOONJAGO_SOX4_TARGETS_UP"
## [1] "SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6"
## [1] "SENESE_HDAC2_TARGETS_UP"
## [1] "KEGG_BLADDER_CANCER"
## [1] "SCHUHMACHER_MYC_TARGETS_UP"
## [1] "KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"
## [1] "REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1"
## [1] "REACTOME_DAG_AND_IP3_SIGNALING"
## [1] "IVANOVSKA_MIR106B_TARGETS"
## [1] "BIOCARTA_RAS_PATHWAY"
## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP"
## [1] "CROMER_METASTASIS_DN"
## [1] "AMIT_EGF_RESPONSE_480_MCF10A"
## [1] "MURAKAMI_UV_RESPONSE_6HR_UP"
## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"
## [1] "LU_EZH2_TARGETS_DN"
## [1] "SESTO_RESPONSE_TO_UV_C2"
## [1] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN"
## [1] "BIOCARTA_CXCR4_PATHWAY"
## [1] "BILD_MYC_ONCOGENIC_SIGNATURE"
## [1] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"
## [1] "LEE_CALORIE_RESTRICTION_NEOCORTEX_DN"
## [1] "REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS"
## [1] "LEONARD_HYPOXIA"
## [1] "COLLER_MYC_TARGETS_UP"
## [1] "BIOCARTA_MTOR_PATHWAY"
## [1] "KEGG_TASTE_TRANSDUCTION"
## [1] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP"
## [1] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"
## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN"
## [1] "SENESE_HDAC1_TARGETS_UP"
## [1] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"
## [1] "ELVIDGE_HIF1A_TARGETS_DN"
## [1] "NAKAMURA_CANCER_MICROENVIRONMENT_DN"
## [1] "PID_DELTA_NP63_PATHWAY"
## [1] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"
## [1] "REACTOME_IL1_SIGNALING"
## [1] "SWEET_KRAS_ONCOGENIC_SIGNATURE"
## [1] "ELVIDGE_HYPOXIA_UP"
## [1] "MANALO_HYPOXIA_UP"
## [1] "WILLERT_WNT_SIGNALING"
## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4"
## [1] "LIAO_METASTASIS"
## [1] "BLUM_RESPONSE_TO_SALIRASIB_UP"
## [1] "AMIT_EGF_RESPONSE_480_HELA"
## [1] "BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN"
## [1] "GROSS_HYPOXIA_VIA_ELK3_DN"
## [1] "KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"
## [1] "BASAKI_YBX1_TARGETS_UP"
## [1] "REACTOME_CA_DEPENDENT_EVENTS"
## [1] "WANG_SMARCE1_TARGETS_DN"
## [1] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN"
## [1] "WEI_MYCN_TARGETS_WITH_E_BOX"
## [1] "PID_A6B1_A6B4_INTEGRIN_PATHWAY"
## [1] "STARK_HYPPOCAMPUS_22Q11_DELETION_UP"
## [1] "GENTILE_RESPONSE_CLUSTER_D3"
## [1] "PID_MTOR_4PATHWAY"
## [1] "DANG_REGULATED_BY_MYC_UP"
## [1] "LI_AMPLIFIED_IN_LUNG_CANCER"
## [1] "LEI_MYB_TARGETS"
## [1] "REACTOME_METABOLISM_OF_NUCLEOTIDES"
## [1] "BIOCARTA_RACCYCD_PATHWAY"
## [1] "SMID_BREAST_CANCER_BASAL_UP"
## [1] "COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP"
## [1] "SMITH_TERT_TARGETS_UP"
## [1] "ALONSO_METASTASIS_EMT_UP"
## [1] "GRANDVAUX_IRF3_TARGETS_DN"
## [1] "KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"
## [1] "REACTOME_PI_METABOLISM"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_DN"
## [1] "CAFFAREL_RESPONSE_TO_THC_24HR_5_UP"
## [1] "NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON"
## [1] "SMIRNOV_RESPONSE_TO_IR_2HR_DN"
## [1] "KEGG_ERBB_SIGNALING_PATHWAY"
## [1] "ZUCCHI_METASTASIS_DN"
## [1] "ZHOU_TNF_SIGNALING_30MIN"
## [1] "PID_TAP63_PATHWAY"
## [1] "KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN"
## [1] "REACTOME_PYRIMIDINE_METABOLISM"
## [1] "NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN"
## [1] "HOFMANN_CELL_LYMPHOMA_UP"
## [1] "BIOCARTA_FMLP_PATHWAY"
## [1] "PID_MYC_ACTIV_PATHWAY"
## [1] "CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN"
## [1] "MOOTHA_GLUCONEOGENESIS"
## [1] "PID_EPHB_FWD_PATHWAY"
## [1] "KIM_WT1_TARGETS_8HR_UP"
## [1] "PID_UPA_UPAR_PATHWAY"
## [1] "SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS"
## [1] "FARMER_BREAST_CANCER_BASAL_VS_LULMINAL"
## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"
## [1] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"
## [1] "NUYTTEN_NIPP1_TARGETS_UP"
## [1] "DOANE_BREAST_CANCER_CLASSES_DN"
## [1] "SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE"
## [1] "CLIMENT_BREAST_CANCER_COPY_NUMBER_UP"
## [1] "THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP"
## [1] "SANA_RESPONSE_TO_IFNG_DN"
## [1] "KEGG_PYRIMIDINE_METABOLISM"
## [1] "KIM_WT1_TARGETS_UP"
## [1] "ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF"
## [1] "FRIDMAN_IMMORTALIZATION_DN"
## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"
## [1] "ZHAN_MULTIPLE_MYELOMA_PR_UP"
## [1] "PHONG_TNF_RESPONSE_VIA_P38_PARTIAL"
## [1] "BIOCARTA_SPPA_PATHWAY"
## [1] "JIANG_HYPOXIA_NORMAL"
## [1] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN"
## [1] "DAZARD_UV_RESPONSE_CLUSTER_G2"
## [1] "RICKMAN_HEAD_AND_NECK_CANCER_D"
## [1] "CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN"
## [1] "PID_CD8_TCR_PATHWAY"
## [1] "GENTILE_UV_RESPONSE_CLUSTER_D5"
## [1] "BILD_HRAS_ONCOGENIC_SIGNATURE"
## [1] "LIM_MAMMARY_STEM_CELL_DN"
## [1] "DITTMER_PTHLH_TARGETS_UP"
## [1] "LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT"
## [1] "WHITFIELD_CELL_CYCLE_G2_M"
## [1] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP"
## [1] "PID_NCADHERIN_PATHWAY"
## [1] "GENTILE_UV_RESPONSE_CLUSTER_D7"
## [1] "PID_HIF1_TFPATHWAY"
## [1] "NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP"
## [1] "GROSS_HYPOXIA_VIA_ELK3_ONLY_UP"
## [1] "NEMETH_INFLAMMATORY_RESPONSE_LPS_UP"
## [1] "LINDGREN_BLADDER_CANCER_CLUSTER_3_DN"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP"
## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP"
## [1] "NUYTTEN_NIPP1_TARGETS_DN"
## [1] "SENESE_HDAC3_TARGETS_UP"
## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_DN"
## [1] "PID_CERAMIDE_PATHWAY"
## [1] "DORSAM_HOXA9_TARGETS_UP"
## [1] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"
## [1] "WANG_LMO4_TARGETS_DN"
## [1] "MOHANKUMAR_HOXA1_TARGETS_DN"
## [1] "ONDER_CDH1_TARGETS_1_DN"
## [1] "BENPORATH_MYC_TARGETS_WITH_EBOX"
## [1] "FERNANDEZ_BOUND_BY_MYC"
## [1] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"
## [1] "KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP"
## [1] "YAGI_AML_WITH_INV_16_TRANSLOCATION"
## [1] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"
## [1] "LINSLEY_MIR16_TARGETS"
## [1] "KEGG_ACUTE_MYELOID_LEUKEMIA"
## [1] "HOELZEL_NF1_TARGETS_UP"
## [1] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"
## [1] "KEGG_PATHWAYS_IN_CANCER"
## [1] "BASSO_HAIRY_CELL_LEUKEMIA_UP"
## [1] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"
## [1] "GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN"
## [1] "BRUINS_UVC_RESPONSE_LATE"
## [1] "MARTINEZ_RB1_TARGETS_UP"
## [1] "DOUGLAS_BMI1_TARGETS_UP"
## [1] "ALFANO_MYC_TARGETS"
## [1] "RAMALHO_STEMNESS_DN"
## [1] "VANASSE_BCL2_TARGETS_DN"
## [1] "REACTOME_DARPP_32_EVENTS"
## [1] "CHANG_CORE_SERUM_RESPONSE_DN"
## [1] "ST_G_ALPHA_I_PATHWAY"
## [1] "REACTOME_RECYCLING_PATHWAY_OF_L1"
## [1] "WILENSKY_RESPONSE_TO_DARAPLADIB"
## [1] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"
## [1] "BIOCARTA_IL7_PATHWAY"
## [1] "REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION"
## [1] "REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL"
## [1] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP"
## [1] "PID_RAC1_REG_PATHWAY"
## [1] "MIKKELSEN_IPS_WITH_HCP_H3K27ME3"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"
## [1] "ROVERSI_GLIOMA_COPY_NUMBER_UP"
## [1] "SCHLOSSER_SERUM_RESPONSE_UP"
## [1] "FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP"
## [1] "MIKKELSEN_IPS_ICP_WITH_H3K27ME3"
## [1] "REACTOME_G_PROTEIN_ACTIVATION"
## [1] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
## [1] "CORRE_MULTIPLE_MYELOMA_DN"
## [1] "REACTOME_GLYCOSPHINGOLIPID_METABOLISM"
## [1] "BIOCARTA_CTLA4_PATHWAY"
## [1] "VECCHI_GASTRIC_CANCER_EARLY_DN"
## [1] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"
## [1] "AKL_HTLV1_INFECTION_DN"
## [1] "KATSANOU_ELAVL1_TARGETS_UP"
## [1] "VALK_AML_WITH_FLT3_ITD"
## [1] "LEIN_MIDBRAIN_MARKERS"
## [1] "HUTTMANN_B_CLL_POOR_SURVIVAL_UP"
## [1] "KEGG_GNRH_SIGNALING_PATHWAY"
## [1] "LEE_LIVER_CANCER_SURVIVAL_UP"
## [1] "LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES"
## [1] "KEGG_MELANOGENESIS"
## [1] "MA_MYELOID_DIFFERENTIATION_DN"
## [1] "REACTOME_REGULATION_OF_INSULIN_SECRETION"
## [1] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"
## [1] "GRADE_COLON_AND_RECTAL_CANCER_DN"
## [1] "ST_ADRENERGIC"
## [1] "CROMER_TUMORIGENESIS_DN"
## [1] "PID_IL3_PATHWAY"
## [1] "REACTOME_G_ALPHA_S_SIGNALLING_EVENTS"
## [1] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"
## [1] "MCCLUNG_COCAINE_REWARD_5D"
## [1] "REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR"
## [1] "ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION"
## [1] "MCCLUNG_DELTA_FOSB_TARGETS_8WK"
## [1] "NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN"
## [1] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"
## [1] "SANSOM_APC_TARGETS_DN"
## [1] "WNT_SIGNALING"
## [1] "KASLER_HDAC7_TARGETS_1_UP"
## [1] "REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY"
## [1] "KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"
## [1] "PEREZ_TP53_TARGETS"
## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP"
## [1] "PEREZ_TP63_TARGETS"